To be clear this will occur after making a built-in change using the toolbar. Anything that requires clicking “Apply Changes” to commit them to the survey theme. You can save changes to the CSS and HTML without issue. Given that there is no good workaround I would use caution, always keep a local version of any CSS or HTML saved on your hard drive in case something goes wrong.
This should be fixed now, everybody. Let us know if you continue to run into any issues.